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Erasing Secrets - How to Remove Sensitive Files from Git History banner

Erasing Secrets - How to Remove Sensitive Files from Git History

Date: 6/15/2025Section: Programming

⚠ Problem

Imagine you accidentally added a sensitive file to Git, committed it, and pushed the repository to GitHub or another platform. After making several more commits, you realize that the file is still being tracked by Git. While you can delete the file and commit the removal, the file remains accessible in the commit history, posing a security risk.

To fully remove the file from the entire Git history, additional steps are required.

✔ Solution

As an example we will remove the .env file from the git history

1. Add the File to .gitignore

First, make sure your .gitignore file contains .env, so it doesn't get tracked again in the future:

echo ".env" >> .gitignore

2. Remove the File from Git History

Use git filter-repo to remove the .env file from all commits

git filter-repo --path .env --invert-paths
info
git-filter-repo command doesn’t come with git by default, you need to install it manually. (Github)

Command breakdown

3. Force Push the Cleaned History

Since we’re modifying the commit history, we need to force push:

git push origin --force --all
This rewrites history, so anyone who has cloned the repo will have to re-clone it.

4. Ensure .env is no Longer in the Repository

Run:

git ls-files | grep .env

or:

git log --stat | grep .env

5. Inform Collaborators

If others have cloned the repo, they need to run:

git fetch origin --prune
git reset --hard origin/main

This forces them to sync with the new cleaned history.

6. (Optional) Remove the File from GitHub Cache

If the .env file was exposed on GitHub, you can also request GitHub to remove cached versions from their servers:

Possible Issues

git: 'filter-repo' is not a git command. See 'git --help'.
Solution
You need to install the git-filter-repo, go to its GitHub repo and follow the installation steps
Aborting: Refusing to destructively overwrite repo history since this does not look like a fresh clone. (expected freshly packed repo) 

Please operate on a fresh clone instead. If you want to proceed anyway, use --force.
Solution
Use --force or work on a fresh clone
git filter-repo --path .env --invert-paths --force

Advanced

Understanding the Command

This command is used to permanently remove the .env file from your Git repository's history. Let's break it down step by step:

Command Breakdown

git filter-repo --path .env --invert-paths
git filter-repo
  • git filter-repo is a modern and more efficient alternative to git filter-branch.
  • It's used for rewriting commit history, particularly for removing files, directories, or sensitive data from a repository.
--path .env
  • This option targets the .env file specifically.
  • It tells git filter-repo that we want to operate on .env (remove it from history).
--invert-paths
  • Inverts the selection, meaning instead of keeping .env, it removes it from all commits.
  • Without --invert-paths, git filter-repo --path .env would only keep .env and remove everything else (which is not what we want).
  • By using --invert-paths, we are saying "remove .env from all commits but keep everything else".

What This Command Does

When you run:

git filter-repo --path .env --invert-paths

it:

  1. Goes through all commits in the repository.
  2. Finds any occurrence of .env in the commit history.
  3. Removes the .env file from those commits (like it was never added in the first place).
  4. Keeps everything else intact.